Contents

1 Cellranger Illumina profiling (190c)

## [1] 27998   190
## [1] 27998   186

## [1] 2000

## Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
## 
## Number of nodes: 186
## Number of edges: 4045
## 
## Running Louvain algorithm...
## Maximum modularity in 10 random starts: 0.7919
## Number of communities: 4
## Elapsed time: 0 seconds

2 Cellranger Illumina profiling (951c)

## [1] 27998   951
## [1] 27998   935

## [1] 2000

## Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
## 
## Number of nodes: 935
## Number of edges: 25447
## 
## Running Louvain algorithm...
## Maximum modularity in 10 random starts: 0.8540
## Number of communities: 9
## Elapsed time: 0 seconds

3 Adding Nanopore data (ISOG/ISO)

4 Integration (RNA)

## Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
## 
## Number of nodes: 1121
## Number of edges: 31187
## 
## Running Louvain algorithm...
## Maximum modularity in 10 random starts: 0.8374
## Number of communities: 10
## Elapsed time: 0 seconds

5 Gene Markers Heatmap

6 Correlation between clusters

7 Clusters re-labelling, saving .rds file

8 Dotplot

9 Gene markers

10 Heatmap

11 Session Info

sessionInfo()
## R version 3.5.2 (2018-12-20)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Debian GNU/Linux 10 (buster)
## 
## Matrix products: default
## BLAS: /usr/lib/x86_64-linux-gnu/openblas/libblas.so.3
## LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.3.5.so
## 
## locale:
##  [1] LC_CTYPE=fr_FR.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=fr_FR.UTF-8        LC_COLLATE=fr_FR.UTF-8    
##  [5] LC_MONETARY=fr_FR.UTF-8    LC_MESSAGES=fr_FR.UTF-8   
##  [7] LC_PAPER=fr_FR.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=fr_FR.UTF-8 LC_IDENTIFICATION=C       
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
##  [1] DoubletFinder_2.0.1 metap_1.1           cowplot_1.0.0      
##  [4] ggrepel_0.8.1       xtable_1.8-4        knitr_1.23         
##  [7] RColorBrewer_1.1-2  forcats_0.4.0       stringr_1.4.0      
## [10] purrr_0.3.2         readr_1.3.1         tidyr_0.8.3        
## [13] tibble_2.1.3        ggplot2_3.2.0       tidyverse_1.2.1    
## [16] pheatmap_1.0.12     dplyr_0.8.3         Seurat_3.0.2       
## [19] BiocStyle_2.10.0   
## 
## loaded via a namespace (and not attached):
##  [1] Rtsne_0.15          colorspace_1.4-1    ggridges_0.5.1     
##  [4] rstudioapi_0.10     listenv_0.7.0       npsurv_0.4-0       
##  [7] lubridate_1.7.4     xml2_1.2.0          codetools_0.2-16   
## [10] splines_3.5.2       R.methodsS3_1.7.1   lsei_1.2-0         
## [13] jsonlite_1.6        broom_0.5.2         ica_1.0-2          
## [16] cluster_2.0.7-1     png_0.1-7           R.oo_1.22.0        
## [19] sctransform_0.2.0   BiocManager_1.30.4  compiler_3.5.2     
## [22] httr_1.4.0          backports_1.1.4     assertthat_0.2.1   
## [25] Matrix_1.2-15       lazyeval_0.2.2      cli_1.1.0          
## [28] htmltools_0.3.6     tools_3.5.2         rsvd_1.0.1         
## [31] igraph_1.2.4.1      gtable_0.3.0        glue_1.3.1         
## [34] RANN_2.6.1          reshape2_1.4.3      Rcpp_1.0.1         
## [37] cellranger_1.1.0    gdata_2.18.0        ape_5.3            
## [40] nlme_3.1-137        gbRd_0.4-11         lmtest_0.9-37      
## [43] xfun_0.8            globals_0.12.4      rvest_0.3.4        
## [46] irlba_2.3.3         gtools_3.8.1        future_1.14.0      
## [49] MASS_7.3-51.1       zoo_1.8-6           scales_1.0.0       
## [52] hms_0.4.2           parallel_3.5.2      yaml_2.2.0         
## [55] reticulate_1.12     pbapply_1.4-0       gridExtra_2.3      
## [58] stringi_1.4.3       caTools_1.17.1.1    bibtex_0.4.2       
## [61] Rdpack_0.11-0       SDMTools_1.1-221.1  rlang_0.4.0        
## [64] pkgconfig_2.0.2     bitops_1.0-6        evaluate_0.14      
## [67] lattice_0.20-38     ROCR_1.0-7          htmlwidgets_1.3    
## [70] labeling_0.3        tidyselect_0.2.5    plyr_1.8.4         
## [73] magrittr_1.5        bookdown_0.11       R6_2.4.0           
## [76] gplots_3.0.1.1      generics_0.0.2      pillar_1.4.2       
## [79] haven_2.1.1         withr_2.1.2         fitdistrplus_1.0-14
## [82] survival_2.43-3     future.apply_1.3.0  tsne_0.1-3         
## [85] modelr_0.1.4        crayon_1.3.4        KernSmooth_2.23-15 
## [88] plotly_4.9.0        rmarkdown_1.13      grid_3.5.2         
## [91] readxl_1.3.1        data.table_1.12.2   digest_0.6.20      
## [94] R.utils_2.9.0       munsell_0.5.0       viridisLite_0.3.0